News

The UK and the genomics race

Published 1 June 10

Genomic technologies are said to have the capacity to
increase the rate of genetic improvement by around 50 percent. But
so far, the UK has shown little sign of participating in the
genomics race and appears to be lagging behind much of the world.
Ann Hardy talked to Marco Winters of DairyCo breeding+ to find out
where we stand today, what genomics can do for UK cattle and if, as
an industry, we can ever catch up.

Why do we need this technology?

We need it because we can improve the rate of genetic gain in
British dairy cows through the use of younger, higher genetic merit
bulls. Estimates of the increased genetic improvement vary from 50
percent to 100 percent, with the precise figure depending on its
uptake and which bulls farmers choose to use. Our estimates at
DairyCo are more conservative at this stage, but even at 15 percent
improvement over the current rate of gain, we estimate a return to
the industry of around £20m in 10 years' time.

The benefits of the genetic gain lie far more in the traits
which are difficult to measure early in a bull's life than in the
production traits. This includes traits such as longevity,
fertility and disease resistance.

The UK uses a high proportion of foreign bulls so can't
we rely on the foreign genomic proofs now coming
through?

I'd use the same arguments against this as I would against the
UK abandoning progeny testing or any genetic evaluation full stop.
For a start, the UK has different breeding objectives from other
countries. And secondly, genetics don't perform in exactly the same
way in different countries. We need to find bulls that are suitable
for UK conditions, so we need UK genomic evaluations.

Furthermore, the UK has some completely different needs from
other countries. For example, few countries will be as interested
in TB resistance as we are, but before we can investigate this, we
need to develop the capabilities to do the genomic evaluations.

It's also worth noting that some other countries' genomic
evaluations are run by commercial companies, which raises the
potential of commercial bias. This is not the case in the UK, where
DairyCo genetic evaluations are completely independent of any
commercial influence.

We hear that the UK is coming from behind in the field
of cattle genomics. What has caused the delay?

When the technology first became available in early 2008,
genotyping and the surrounding R&D was undertaken very much on
a country by country basis and was driven by the large
multi-national breeding companies wishing to make a more informed
choice about bulls entering progeny test. The major benefit
appeared to lie with the AI companies, the costs involved were
extremely high at the time - potentially running into millions -
and it was not something DairyCo felt able to recommend UK dairy
farmers should invest in at that stage and cost. At the time, there
was also a general unwillingness to share resources, so if we as a
country had wanted to be involved, we would have had to do it on
our own.

However, behind the scenes, we were undertaking background work
with EGENES - the Edinburgh Genetic Evaluation Services which is
led by Dr Mike Coffey and based at SAC - who carry out genetic
evaluations on DairyCo's behalf and have been leading an
international consortium (called Clubware) to develop the relevant
software.

So what's the position today?

Early last year, the mood completely changed as the countries
involved realised that it was too big a task for each of them to
manage on their own. The technology stands or falls by the numbers
of animals genotyped and the more bulls you can get into your
reference population, the better. A few thousand will get you
started, but ideally, you'd like 10,000 animals in this population,
so clearly collaboration across borders was going to be needed to
meet this goal.

As the magnitude of the task became apparent, so a general
willingness for the UK to take part in a shared approach
increased.

Meanwhile, Cogent and Genus had been investing in genotyping a
large number of their own bulls, but would never be able to obtain
genomically enhanced UK evaluations while there was no SNP-key for
the UK.

But an industry group within the UK now feels the time is right
to become involved in developing a SNP-key for the UK, so allowing
British farmers to benefit from genomically enhanced UK
evaluations.

This collaboration is being driven by DairyCo - who the industry
partners have appointed as the custodians of the information - and
will be developed together with our partners at EGENES. It also
involves Cogent and Genus as well as all those organisations who
contribute data to UK genetic evaluations. This currently includes
NMR, CIS, UDF and Holstein UK.

The DairyCo board has committed some money, which will be used
to get Clubware software fully operational and develop a genotype
bank to enable genomic evaluations to be carried out by EGENES. At
the same time, DEFRA has also committed some funding towards
providing genotypes through an initiative known as the Ruminant
Genetic Improvement Network.

The benefit of this is that we are now already in a position to
start pooling and swapping genotypes with other countries.

Does it mean we will have a reference population of
animals in the UK?

Thanks to the investment of Cogent, Genus and DEFRA, alongside
the opportunity to collaborate with other international partners,
we have already started to build up this population and within a
few months, we hope to have around 3,000 bulls in our genotype bank
and we continue to explore opportunities to increase this further
over the next few months.

But is the UK in a position to ever catch
up?

Absolutely. Remember, at this stage we're only a year behind the
very first countries to have genomic evaluations available, and
because the technology is now in its second phase, we may well be
at a small advantage. As of last month, a new high density SNP-chip
has become available which measures over 800,000 SNPs. This
compares with 54,000 in the previous chip which means it will be
far more informative. It also means that over 1,000 bulls used in
the UK will be genotyped with this high density chip whereas some
other countries may have to re-genotype some of their bulls which
were previously tested with the lower density chip.

At the same time, the costs involved have plummeted, which means
that the UK industry can obtain far more information at a
relatively low cost.

What information will be available?

We will be able to provide genomically enhanced evaluations
immediately for all traits we currently measure and evaluate.
Alongside these, there will be the potential for some new traits to
be evaluated, such as disease resistance (eg for Johne's and TB,
which are known to be heritable), as well as fatty acid profiles in
the milk indicating saturated versus unsaturated fats, and
potentially even feed conversion efficiency. In time, there might
even be scope to develop genomically enhanced indexes for traits
such as methane production.

How will the evaluations be expressed?

The USA expresses genomically enhanced Predicted Transmitting
Abilities as gPTAs and the UK is likely to do the same. The 'g'
signifies a genomic component to the index, alongside the usual
parent and ancestry element. Eventually, daughter information will
take over in importance from the genomic and ancestry information,
although these will remain a small and diminishing component of a
proof.

Can the technology be used for a farmer's own
livestock?

Definitely. If a farmer wants to select replacements for his own
herd, he will be able to genotype, say, two full sisters at birth
to find out which is best. Although they will both have the same
parent average (Pedigree Index) information, they could have quite
different genotypes, and one may have far better prospects for
things like milk production, fertility, cell counts or lifespan. We
are now able to confidently say that the genomically enhanced
evaluation will be far more reliable than a Pedigree Index, so the
test could be worthwhile for many breeders and could have a
worthwhile payback over the cow's lifetime.

How much is the test likely to cost?

We've spoken about the new high density chip which will still be
quite expensive, but alongside it, a low density chip - of only
about 3,000 SNPs - has also been developed. Although this sort of
SNP-chip will provide less information on its own, as part of the
wider system it will probably be adequate for selection purposes.
It's not possible to say at this stage what its cost will be, but
I'd estimate that the full test will be around £50.

What about the breeds other than Holstein?

The current technology only works within breeds, and therefore
the smaller populations are not yet able to benefit from the work
being done by the Holstein breeding industry. However, the new,
high density SNP-chip is expected to change that, which hopefully
will unlock the potential to use the same SNP-key across different
breeds, including crossbreds. The UK, as one of only a few
countries in the world to provide an all-breed genetic evaluation
system, launched earlier this year, is therefore ideally placed to
capture the full potential for all breeds.

So when will we have genomic evaluations for the
UK?

We are aiming to have official genomically enhanced evaluations
for bulls in the UK in 2011.

Glossary

Genome - The entire complement of the animal's
genetic material.

Genomics - the study of an animal's genome
functions.

Genotype - The measure of an animal's genetic
makeup.

Phenotype- The observable
physical traits of an animal (such as stature or milk yield) which
is a combination of both its genetic makeup and environmental
influences.

Reference population - A population of several
thousand animals whose actual performance and genotype are compared
to establish relationships between the two. From these
relationships, a SNP-key can be devised.

SNP (SingleNucleotide Polymorphism)
- A measurement of genetic variation, which can be used to
describe an animal's genotype.

SNP-chip - A means of measuring different
SNPs.

SNP-key - A key, which is specific to a
cattle population, which 'unlocks' or translates an animal's
genotype, as measured by the SNP-chip, into a genetic index such as
a genomic Predicted Transmitting Ability (gPTA).